In order to migrate an Extension from a version prior to 3.1 and recreate the mentioned Resources hierarchy, follow these steps:

Open the Extension with Integration Studio;

Click the Resources tree tab (second tab of the left tree):

If the Extension already included the source code as Resources (formerly dependencies), the upgrade have already taken care of the entire migration process. You should be able to see, in the Resources tree, a hierarchy similar to the one presented in the post Extensions Source Code Management With Integration Studio. You can stop the recipe here;

If the Extension didn't include source code as Resources (formerly dependencies), proceed with the recipe;

Right-Click the Resources folder and select the "Open" option. An explorer window will open;

Make sure you see a folder named Source in the opened explorer window:

If this folder doesn't exists, create it;

Locate the source code of your Extension and copy it to the Source folder mentioned in the previous step;

Open the Extension's project with Microsoft Visual Studio:

Double click the HeExt<ExtensionName>.csproj file;

Open the Solution Explorer tree:

Press "Ctrl-Alt-L";

Rename the solution to <ExtensionName>:

Right-click the tree root and select "Rename";

Rename the project to <ExtensionName>:

Right-click the Extension's project node and select "Rename";

Perform the following renames to the files presented inside the Extension's project:

HeExt<ExtensionName>.cs to <ExtensionName>.cs;

Iss<ExtensionName>.cs to Interface.cs;

Close Microsoft Visual Studio:

Answer "Yes" when asked to save <ExtensionName>.sln and childs;

Go back to Integration Studio;

Click the Resources tree tab (second tab on the left tree):

You should now see the Extension's source files in the Resources tree;

Right-click the <ExtensionName>.cs and select the "Include in Extension" option;

Verify and Save the Extension:

Press "F4";

Your Extension should have been Verified, Compiled and Saved:

During this process all the remaining source code files were included as Extension Resources and the Extension's .Net Assembly was recompiled;